Learn about the tools, processes and analysis approaches used in the field of metagenomics.

This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data; including marker gene, whole gene shotgun (WGS) and assembly-based approaches.

The virtually-delivered content will involve participants learning via pre-recorded lectures and live presentations, followed by live Q&As with the trainers. Practical experience will be developed in group activities and in computational exercises run in Docker containers on our virtual training infrastructure.

Participants will need to be available between the hours of 09:00-17:00 GMT each day of the course.

Who is this course for?

This course is aimed at life scientists who are working in the field of metagenomics and are currently in the early stages of data analysis. Participants should have some prior experience of using bioinformatics in their research.

The practical sessions in the course require a basic understanding of the Unix command line and the R statistics package. If you are not already familiar with these then please ensure that you complete these free tutorials before you attend the course:

• Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
• Basic R concept tutorials: www.r-tutor.com/r-introduction

What will I learn?

Learning outcomes

After this course you should be able to:

• Conduct appropriate quality control and decontamination of metagenomic data and run simple assembly pipelines on short read data
• Utilise public datasets and resources to identify relevant data for analysis
• Apply relevant tools in the analysis of metagenomic data
• Submit metagenomics data to online repositories for sharing and future analysis
• Apply knowledge in the areas of strain resolution and additional functional analysis

Course content

During this course you will learn about:

• Different types of microbiome data:
  • Amplicon approaches (ribosomal RNA)
  • Whole genome shotgun (WGS) approaches
• Assembly and metagenome assembled genomes (MAGs)
• Data analysis: MGnify, HMMER, InterPro, GO, FASTQC, and pathway analyses
• Data standards and submission:
  • European Nucleotide Archive (ENA)
  • Genomic Standards Consortium (GSC)
  • SRA
  • Webin
• Microbiome data analysis workflow

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form providing answers as directed
• Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs that cover your:
  • scientific biography/work experience
  • current research interests
• Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by 23:59 GMT, Friday 3rd September.

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Monday 27 September.

Participant flash talks

There will be an opportunity for all participants to give a short presentation as part of the course covering their work. These will offer a chance to share research with the other participants and an opportunity for them and trainers to ask questions. Further details will be provided following registration.